Code
if(base::interactive()) {
params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interestWhere we analyse the effect of a factor on local diversity
Date: December 2, 2024
See the documentation of the MiscMetabar package for example of alpha diversity analysis.
if(base::interactive()) {
params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interestlibrary(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/02_alpha_diversity.qmd")
source(here::here("R/styles.R"))d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))Cleaning suppress 0 taxa and 26 samples.
hill_pq(subset_samples(d_pq, Type %in% c("Mix", "Mono")), factor_of_interest, one_plot = TRUE) &
(
theme_idest(
subtitle_size = 8,
plot_title_size = 12,
plot_margin = margin(5, 10, 5, 10),
axis_title_size = 9,
axis_text_size = 8
) + theme(legend.position = "none")
) Error in h(simpleError(msg, call)): erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction '%in%' : objet 'Type' introuvable
MiscMetabar::accu_plot_balanced_modality(d_pq, factor_of_interest, nperm=20) + theme_idest()`set.seed(1)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(1); .Random.seed` for the full vector
...
Error in validObject(.Object): objet de classe "sample_data" incorrect: Sample Data must have non-zero dimensions.
ggbetween_pq(d_pq, factor_of_interest)Error in h(simpleError(msg, call)): erreur d'�valuation de l'argument 'object' lors de la s�lection d'une m�thode pour la fonction 'sample_data' : colonnes non définies sélectionnées
Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data_final/information_run.txt .
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] MiscMetabar_0.10.1 purrr_1.0.2 dplyr_1.1.4 dada2_1.34.0
[5] Rcpp_1.0.13-1 ggplot2_3.5.1 phyloseq_1.50.0 targets_1.9.0
[9] knitr_1.49
loaded via a namespace (and not attached):
[1] bitops_1.0-9 deldir_2.0-4
[3] permute_0.9-7 rlang_1.1.4
[5] magrittr_2.0.3 ade4_1.7-22
[7] matrixStats_1.4.1 compiler_4.4.2
[9] mgcv_1.9-1 png_0.1-8
[11] callr_3.7.6 vctrs_0.6.5
[13] reshape2_1.4.4 stringr_1.5.1
[15] pwalign_1.2.0 pkgconfig_2.0.3
[17] crayon_1.5.3 fastmap_1.2.0
[19] backports_1.5.0 XVector_0.46.0
[21] utf8_1.2.4 Rsamtools_2.22.0
[23] rmarkdown_2.29 UCSC.utils_1.2.0
[25] ps_1.8.1 xfun_0.49
[27] zlibbioc_1.52.0 GenomeInfoDb_1.42.1
[29] jsonlite_1.8.9 biomformat_1.34.0
[31] rhdf5filters_1.18.0 DelayedArray_0.32.0
[33] Rhdf5lib_1.28.0 BiocParallel_1.40.0
[35] jpeg_0.1-10 parallel_4.4.2
[37] cluster_2.1.6 R6_2.5.1
[39] RColorBrewer_1.1-3 stringi_1.8.4
[41] GenomicRanges_1.58.0 SummarizedExperiment_1.36.0
[43] iterators_1.0.14 IRanges_2.40.0
[45] Matrix_1.7-1 splines_4.4.2
[47] igraph_2.1.1 tidyselect_1.2.1
[49] rstudioapi_0.17.1 abind_1.4-8
[51] yaml_2.3.10 vegan_2.6-8
[53] codetools_0.2-20 hwriter_1.3.2.1
[55] processx_3.8.4 lattice_0.22-6
[57] tibble_3.2.1 plyr_1.8.9
[59] Biobase_2.66.0 withr_3.0.2
[61] ShortRead_1.64.0 evaluate_1.0.1
[63] survival_3.7-0 RcppParallel_5.1.9
[65] Biostrings_2.74.0 pillar_1.9.0
[67] BiocManager_1.30.25 MatrixGenerics_1.18.0
[69] renv_1.0.11 foreach_1.5.2
[71] stats4_4.4.2 generics_0.1.3
[73] rprojroot_2.0.4 S4Vectors_0.44.0
[75] munsell_0.5.1 scales_1.3.0
[77] base64url_1.4 glue_1.8.0
[79] tools_4.4.2 interp_1.1-6
[81] data.table_1.16.2 GenomicAlignments_1.42.0
[83] rhdf5_2.50.0 grid_4.4.2
[85] ape_5.8 latticeExtra_0.6-30
[87] colorspace_2.1-1 nlme_3.1-166
[89] GenomeInfoDbData_1.2.13 cli_3.6.3
[91] fansi_1.0.6 S4Arrays_1.6.0
[93] gtable_0.3.6 digest_0.6.37
[95] BiocGenerics_0.52.0 SparseArray_1.6.0
[97] htmlwidgets_1.6.4 htmltools_0.5.8.1
[99] multtest_2.62.0 lifecycle_1.0.4
[101] here_1.0.1 httr_1.4.7
[103] secretbase_1.0.3 MASS_7.3-61
@online{taudière2024,
author = {Taudière, Adrien},
title = {Alpha-Diversity},
date = {2024-12-02},
langid = {en}
}